FLC OF AN LGT UNDERSHOT XING ALT FIX DUE TO AN FMS PROGRAM PROB.

Narrative

WHEN LOADING THE FMS ON PREFLT; THE FMS DATABASE REVEALED 2 BARET. BARET 4 STARS 'BAR 09' AND 'BAR 27.' I SELECTED 'BAR 27' BUT MY CDU DISPLAY JUMPED FROM 'IPL' TO 'SWATT' INTXN. I THEN MANUALLY TYPED IN THE INTXNS AFTER 'IPL': 'KUMBA;' 'PILLO' 'BARET' 'PGY04305.' THEN I FILLED IN THE 'SWATT' INTXN TO CLOSE THE DISCONTINUITY. THE FLT PLAN WAS ACTIVATED. ENRTE; I TYPED IN THE XING RESTR OF 10000 FT AT 'PILLO.' ON LETDOWN I DISCOVER (TOO LATE) THAT ALTHOUGH THE 'PILLO' 10000 FT RESTR IS STILL ON THE 'LEGS' PAGE AND 'PILLO' IS THE FIRST CHK POINT ON THE PAGE; THE FMS HAS SELECTED 'BARET' AS THE ACTIVE WAYPOINT. THE 'DES' PAGE SHOWED THE ACFT ON PROFILE; BUT I'M ONLY 10 MI E OF 'PILLO' AT 16000 FT. WE INFORMED LA ARTCC WE WOULD NOT BE ABLE TO CROSS 'PILLO' AT 10000 FT; AND THEIR REPLY WAS 'CONTACT SAN DIEGO APCH CTL ON FREQ XXXXX.' CHKED IN WITH SAN DIEGO APCH CTL AND TOLD THEM WE WOULD BE HIGH AT 'PILLO' AND THEY PUT US ON A VECTOR FOR LINDBERGH. I DO NOT UNDERSTAND WHY THE FMS DID WHAT IT DID.